uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
PDB_REDO: automated re-refinement of X-ray structure models in the PDB
Show others and affiliations
2009 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 42, 376-384 p.Article in journal (Refereed) Published
Abstract [en]

Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.

Place, publisher, year, edition, pages
2009. Vol. 42, 376-384 p.
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-129054DOI: 10.1107/S0021889809008784ISI: 000266268300002OAI: oai:DiVA.org:uu-129054DiVA: diva2:337515
Available from: 2010-08-06 Created: 2010-08-05 Last updated: 2013-11-01Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text
By organisation
Department of Cell and Molecular Biology
In the same journal
Journal of applied crystallography
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 170 hits
ReferencesLink to record
Permanent link

Direct link